The primary nucleotide sequence of two defective variants of SV40 that contain covalently linked monkey sequences has been determined. The structures around the joints between SV40 and monkey DNA in these variants indicate that mechanisms other than those depending on extensive homology between recombining molecules were responsible for recombination. Studies on the transcription of these defective variants in infected cells indicate that they are transcribed even though they contain only very short regions of the wild type viral genome. New approaches to the isolation of substituted defective molecules have been devised. One of these approaches allows the isolation of defective variants containing monkey sequences even when they occur in only a few out of 10 to the 6th power infected cells. The newly isolated variants appear to be quite similar in structure to one of the two we studied earlier. Studies on the structure of the new isolates is being facilitated by means of recombinant DNA techniques.